The work aims to achieve efficient flatness processing of metal molybdenum wafers and obtain a super smooth surface. Free abrasives were used to lap the molybdenum wafers. The influences of abrasive types, lapping disc rotation speed, lapping pressure and lapping time on the lapping effect were studied. Through modeling analysis of material removal rate (MRR) and the surface roughness (Ra), a comparison was made between molybdenum and highly hard-brittle and highly plastic materials to reveal their lapping properties and explore the mechanism of surface formation. The results showed that the comprehensive effect of factors on the removal rate, surface morphology forming of molybdenum wafer materials. CeO2 abrasive was suitable for lapping molybdenum wafer substrates. Material removal occurred through two-body and three-body frictional plastic removal mechanisms. The MRR during the lapping process increased first and then decreased with the increase of lapping disc rotation speed and lapping pressure. The MRR reached its maximum at 60 r/min and 0.026 MPa. Surface roughness showed minimal variation with different process parameters, except for the abrasive factor. Both MRR and Ra tended to stabilize with the increase in lapping time. By using W1 CeO2 abrasive with a particle size, a flat surface was achieved by lapping for 40 minutes at a lapping disc rotation speed of 60 r/min and a lapping pressure of 0.026 MPa, reducing the surface roughness from Ra 46 nm to Ra 9.53 nm, with MRR of 1.16 mg/min. By using the free abrasive lapping method, the surface roughness of molybdenum wafers can be effectively reduced, thus consistently achieving the desired surface for applications, under optimized process parameters.